comparison between groups with heavy peptides spiked

comparison between groups with heavy peptides spiked io  2021-05-06

Dear all,
I have samples of 5 different conditions
I have spiked heavy peptides into different amounts in each group of samples (to have a ratio light/heavy of 1 approx) but not a calibration curve.
What is the best results table to do the quantification and to see the significant differences?
Thank you in advance

Nick Shulman responded:  2021-05-25
I am not sure I understand your question.

Are you saying that you would like your normalization method to be "ratio to heavy", but the amount of heavy that was spiked into each sample depends on the condition?
One thing that you could do is an ordinary Group Comparison in Skyline, using the normalization method "Ratio to Heavy". But, then, you would need to manually multiple the fold change results that Skyline gives you by a factor which depends on the heavy concentration in the two samples.

Is that what you are asking?

If you would like, you can send us your Skyline document and we might understand better what you are asking.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

-- Nick
io responded:  2021-05-26
Thank you very much Nick,
Yes, this was the question.
I have repeated the experiment with the same concentration of heavy peptide in all the conditions, so I assume I can do "Ratio to heavy" normalization.
I do Other Grids, Group Comparison, in Settings Normalization method Ratio to Heavy.